STOCHASTIC DYNAMICS SIMULATION OF ALANINE DIPEPTIDE - INCLUDING SOLVATION INTERACTION DETERMINED BY BOUNDARY-ELEMENT METHOD

A merger of the Poisson-Boltzmann equation and stochastic dynamics sim ulation is examined using illustrative calculations of alanine dipepti de. The boundary element method (BEM) is used to calculate the hydrati on forces acting on the solute molecule based on the surroundings. Com putational efficiency is achieved by the use of a simple hydration mod el and a coarse boundary element. Nonetheless, the conformational dist ribution obtained from this new method is reasonable compared with oth er theoretical and computational results. Detailed analysis has been a ccomplished in terms of the hydration interactions and solvation energ ies. The results indicate that the new simulation method provides an o bvious improvement over the conventional stochastic dynamics simulatio n technique. The further improvement of the hydration model and future application to large molecules are also discussed. (C) 1997 John Wile y & Sons, Inc.